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Add a new script to assemble amplicon from solexa pair-end run

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This commit is contained in:
Eric Coissac
2010-01-15 10:56:51 +00:00
parent b93d5ced56
commit e560c4296b
25 changed files with 14802 additions and 1336 deletions
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3
src/obitools/align/__init__.py
View File

@@ -3,4 +3,7 @@
from _nws import NWS
from _lcs import LCS
from _assemble import DirectAssemble, ReverseAssemble
from _qsassemble import QSolexaDirectAssemble,QSolexaReverseAssemble
from _rassemble import RightDirectAssemble as RightReverseAssemble
from _qsrassemble import QSolexaRightDirectAssemble,QSolexaRightReverseAssemble

743
src/obitools/align/_assemble.c
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File diff suppressed because it is too large Load Diff

10
src/obitools/align/_assemble.pxd Normal file
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@@ -0,0 +1,10 @@
from _nws cimport *
cdef class DirectAssemble(NWS):
cdef double ysmax
cdef int ymax
cdef double doAlignment(self) except? 0
cdef class ReverseAssemble(DirectAssemble):
pass

48
src/obitools/align/_assemble.pyx
View File

@@ -5,25 +5,22 @@ Created on 6 Nov. 2009
'''
#@PydevCodeAnalysisIgnore
from _nws cimport *
from _assemble cimport *
cdef class DirectAssemble(NWS):
cdef double ysmax
cdef int ymax
def __init__(self,match=4,mismatch=-6,opengap=-8,extgap=-2):
NWS.__init__(self,match,mismatch,opengap,extgap)
self.ysmax=0
self.ymax=0
cdef double matchScore(self,int h, int v):
return iupacPartialMatch(self.hSeq.sequence[h-1],self.vSeq.sequence[v-1])
cdef double doAlignment(self) except? 0:
cdef int i # vertical index
cdef int j # horizontal index
cdef int idx
cdef int idx0
cdef int idx1
cdef int jump
cdef int delta
cdef double score
@@ -34,6 +31,8 @@ cdef class DirectAssemble(NWS):
if self.needToCompute:
self.allocate()
self.reset()
self.ysmax=0
self.ymax=0
for j in range(1,self.hSeq.length+1):
idx = self.index(j,0)
@@ -45,11 +44,16 @@ cdef class DirectAssemble(NWS):
self.matrix.matrix[idx].score = self._opengap + (self._extgap * (i-1))
self.matrix.matrix[idx].path = -i
idx0=self.index(-1,0)
idx1=self.index(0,1)
for i in range(1,self.vSeq.length+1):
idx0+=1
idx1+=1
for j in range(1,self.hSeq.length+1):
# 1 - came from diagonal
idx = self.index(j-1,i-1)
#idx = self.index(j-1,i-1)
idx = idx0
# print "computing cell : %d,%d --> %d/%d" % (j,i,self.index(j,i),self.matrix.msize),
scoremax = self.matrix.matrix[idx].score + \
self.matchScore(j,i)
@@ -58,7 +62,8 @@ cdef class DirectAssemble(NWS):
# print "so=%f sd=%f sm=%f" % (self.matrix.matrix[idx].score,self.matchScore(j,i),scoremax),
# 2 - open horizontal gap
idx = self.index(j-1,i)
# idx = self.index(j-1,i)
idx = idx1 - 1
score = self.matrix.matrix[idx].score+ \
self._opengap
if score > scoremax :
@@ -66,7 +71,8 @@ cdef class DirectAssemble(NWS):
path = +1
# 3 - open vertical gap
idx = self.index(j,i-1)
# idx = self.index(j,i-1)
idx = idx0 + 1
score = self.matrix.matrix[idx].score + \
self._opengap
if score > scoremax :
@@ -95,7 +101,8 @@ cdef class DirectAssemble(NWS):
scoremax = score
path = -delta-1
idx = self.index(j,i)
# idx = self.index(j,i)
idx = idx1
self.matrix.matrix[idx].score = scoremax
self.matrix.matrix[idx].path = path
@@ -107,14 +114,16 @@ cdef class DirectAssemble(NWS):
if j==self.hSeq.length and scoremax > self.ysmax:
self.ysmax=scoremax
self.ymax=i
idx0+=1
idx1+=1
self.sequenceChanged=False
self.scoreChanged=False
return self.ysmax
def backtrack(self):
cdef list path=[]
cdef void backtrack(self):
#cdef list path=[]
cdef int i
cdef int j
cdef int p
@@ -122,13 +131,17 @@ cdef class DirectAssemble(NWS):
self.doAlignment()
i=self.ymax
j=self.hSeq.length
self.path=allocatePath(i,j+1,self.path)
if self.ymax<self.vSeq.length:
path.append(self.ymax-self.vSeq.length)
self.path.path[self.path.length]=self.ymax-self.vSeq.length
self.path.length+=1
while (i or j):
p=self.matrix.matrix[self.index(j,i)].path
path.append(p)
self.path.path[self.path.length]=p
self.path.length+=1
#path.append(p)
if p==0:
i-=1
j-=1
@@ -137,8 +150,11 @@ cdef class DirectAssemble(NWS):
else:
j-=p
path.reverse()
return 0,0,path
#path.reverse()
#reversePath(self.path)
self.path.hStart=0
self.path.vStart=0
#return 0,0,path
cdef class ReverseAssemble(DirectAssemble):

1432
src/obitools/align/_dynamic.c
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File diff suppressed because it is too large Load Diff

19
src/obitools/align/_dynamic.pxd
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@@ -39,6 +39,20 @@ cdef alignSequence* allocateSequence(object bioseq, alignSequence* seq=?)
cdef void freeSequence(alignSequence* seq)
cdef struct alignPath:
long length
long buffsize
long vStart
long hStart
long *path
cdef alignPath* allocatePath(long l1,long l2,alignPath* path=?)
cdef void reversePath(alignPath* path)
cdef void freePath(alignPath* path)
cdef int bitCount(int x)
cpdef bint iupacMatch(unsigned char a, unsigned char b)
@@ -52,6 +66,7 @@ cdef class DynamicProgramming:
cdef alignSequence* hSeq
cdef alignSequence* vSeq
cdef alignPath* path
cdef double _opengap
cdef double _extgap
@@ -65,5 +80,7 @@ cdef class DynamicProgramming:
cdef double matchScore(self,int h, int v)
cdef double doAlignment(self) except? 0
cdef void reset(self)
cdef inline int index(self,x,y)
cdef inline int index(self, int x, int y)
cdef inline bint _needToCompute(self)
cdef void backtrack(self)

62
src/obitools/align/_dynamic.pyx
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@@ -18,6 +18,7 @@ from obitools.alignment import Alignment
#
from _dynamic cimport *
from Cython.Shadow import NULL
cdef AlignMatrix* allocateMatrix(int hsize, int vsize,AlignMatrix *matrix=NULL):
@@ -104,6 +105,39 @@ cdef void freeSequence(alignSequence* seq):
free(<void*>seq.quality)
free(seq)
cdef alignPath* allocatePath(long l1,long l2,alignPath* path=NULL):
cdef long length=l1+l2
if path is NULL:
path = <alignPath*>malloc(sizeof(alignPath))
path.length=0
path.buffsize=0
path.path=NULL
if length > path.buffsize:
path.buffsize=length
path.path=<long*>realloc(path.path,sizeof(long)*length)
path.length=0
path.vStart=0
path.hStart=0
return path
cdef void reversePath(alignPath* path):
cdef long i
cdef long j
j=path.length
for i in range(path.length/2):
j-=1
path.path[i],path.path[j]=path.path[j],path.path[i]
cdef void freePath(alignPath* path):
if path is not NULL:
if path.path is not NULL:
free(<void*>path.path)
free(<void*>path)
cdef int aascii = ord(b'a')
@@ -139,6 +173,7 @@ cdef class DynamicProgramming:
self.matrix=NULL
self.hSeq=NULL
self.vSeq=NULL
self.path=NULL
self.horizontalSeq=None
self.verticalSeq=None
@@ -164,6 +199,12 @@ cdef class DynamicProgramming:
cdef double doAlignment(self) except? 0:
pass
cdef bint _needToCompute(self):
return self.scoreChanged or self.sequenceChanged
cdef void backtrack(self):
pass
property seqA:
def __get__(self):
return self.horizontalSeq
@@ -210,7 +251,7 @@ cdef class DynamicProgramming:
self.scoreChanged=True
resetMatrix(self.matrix)
cdef inline int index(self,x,y):
cdef inline int index(self, int x, int y):
return (self.hSeq.length+1) * y + x
@@ -219,6 +260,7 @@ cdef class DynamicProgramming:
freeMatrix(self.matrix)
freeSequence(self.hSeq)
freeSequence(self.vSeq)
freePath(self.path)
def __call__(self):
cdef list hgaps=[]
@@ -229,13 +271,15 @@ cdef class DynamicProgramming:
cdef int lenh=0
cdef int lenv=0
cdef int h,v,p
cdef int i
cdef object ali
cdef double score
if self.needToCompute:
if self._needToCompute():
score = self.doAlignment()
h,v,b=self.backtrack()
for p in b:
self.backtrack()
for i in range(self.path.length-1,-1,-1):
p=self.path.path[i]
if p==0:
hp+=1
vp+=1
@@ -258,7 +302,7 @@ cdef class DynamicProgramming:
vgaps.append([vp,0])
if lenh < self.hSeq.length:
hseq=self.horizontalSeq[h:h+lenh]
hseq=self.horizontalSeq[self.path.hStart:self.path.hStart+lenh]
else:
hseq=self.horizontalSeq
@@ -266,7 +310,7 @@ cdef class DynamicProgramming:
hseq.gaps=hgaps
if lenv < self.vSeq.length:
vseq=self.verticalSeq[v:v+lenv]
vseq=self.verticalSeq[self.path.vStart:self.path.vStart+lenv]
else:
vseq=self.verticalSeq
@@ -276,10 +320,12 @@ cdef class DynamicProgramming:
ali=Alignment()
ali.append(hseq)
ali.append(vseq)
ali.score=score
self.alignment=ali
return self.alignment.clone()
ali=self.alignment.clone()
ali.score=self.alignment.score
return ali

346
src/obitools/align/_lcs.c
View File

@@ -1,4 +1,4 @@
/* Generated by Cython 0.11.3 on Sun Nov 8 08:26:04 2009 */
/* Generated by Cython 0.11.3 on Mon Jan 4 22:18:11 2010 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -335,6 +335,11 @@ static INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *);
static INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *);
static INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
static INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
static void __Pyx_WriteUnraisable(const char *name); /*proto*/
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, long size); /*proto*/
static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
@@ -423,7 +428,36 @@ struct __pyx_opt_args_8obitools_5align_8_dynamic_allocateSequence {
struct __pyx_t_8obitools_5align_8_dynamic_alignSequence *seq;
};
/* "/Users/coissac/encours/OBITools/src/obitools/align/_dynamic.pxd":47
/* "/Users/coissac/encours/OBITools/src/obitools/align/_dynamic.pxd":42
* cdef void freeSequence(alignSequence* seq)
*
* cdef struct alignPath: # <<<<<<<<<<<<<<
* long length
* long buffsize
*/
struct __pyx_t_8obitools_5align_8_dynamic_alignPath {
long length;
long buffsize;
long vStart;
long hStart;
long *path;
};
/* "/Users/coissac/encours/OBITools/src/obitools/align/_dynamic.pxd":49
* long *path
*
* cdef alignPath* allocatePath(long l1,long l2,alignPath* path=?) # <<<<<<<<<<<<<<
*
* cdef void reversePath(alignPath* path)
*/
struct __pyx_opt_args_8obitools_5align_8_dynamic_allocatePath {
int __pyx_n;
struct __pyx_t_8obitools_5align_8_dynamic_alignPath *path;
};
/* "/Users/coissac/encours/OBITools/src/obitools/align/_dynamic.pxd":61
* cpdef double iupacPartialMatch(unsigned char a, unsigned char b)
*
* cdef class DynamicProgramming: # <<<<<<<<<<<<<<
@@ -439,6 +473,7 @@ struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming {
PyObject *verticalSeq;
struct __pyx_t_8obitools_5align_8_dynamic_alignSequence *hSeq;
struct __pyx_t_8obitools_5align_8_dynamic_alignSequence *vSeq;
struct __pyx_t_8obitools_5align_8_dynamic_alignPath *path;
double _opengap;
double _extgap;
PyObject *alignment;
@@ -459,7 +494,7 @@ struct __pyx_obj_8obitools_5align_4_lcs_LCS {
};
/* "/Users/coissac/encours/OBITools/src/obitools/align/_dynamic.pxd":47
/* "/Users/coissac/encours/OBITools/src/obitools/align/_dynamic.pxd":61
* cpdef double iupacPartialMatch(unsigned char a, unsigned char b)
*
* cdef class DynamicProgramming: # <<<<<<<<<<<<<<
@@ -472,7 +507,9 @@ struct __pyx_vtabstruct_8obitools_5align_8_dynamic_DynamicProgramming {
double (*matchScore)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *, int, int);
double (*doAlignment)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *);
void (*reset)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *);
int (*index)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *, PyObject *, PyObject *);
int (*index)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *, int, int);
int (*_needToCompute)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *);
void (*backtrack)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *);
};
static struct __pyx_vtabstruct_8obitools_5align_8_dynamic_DynamicProgramming *__pyx_vtabptr_8obitools_5align_8_dynamic_DynamicProgramming;
@@ -497,6 +534,9 @@ static void (*__pyx_f_8obitools_5align_8_dynamic_freeMatrix)(struct __pyx_t_8obi
static void (*__pyx_f_8obitools_5align_8_dynamic_resetMatrix)(struct __pyx_t_8obitools_5align_8_dynamic_AlignMatrix *); /*proto*/
static struct __pyx_t_8obitools_5align_8_dynamic_alignSequence *(*__pyx_f_8obitools_5align_8_dynamic_allocateSequence)(PyObject *, struct __pyx_opt_args_8obitools_5align_8_dynamic_allocateSequence *__pyx_optional_args); /*proto*/
static void (*__pyx_f_8obitools_5align_8_dynamic_freeSequence)(struct __pyx_t_8obitools_5align_8_dynamic_alignSequence *); /*proto*/
static struct __pyx_t_8obitools_5align_8_dynamic_alignPath *(*__pyx_f_8obitools_5align_8_dynamic_allocatePath)(long, long, struct __pyx_opt_args_8obitools_5align_8_dynamic_allocatePath *__pyx_optional_args); /*proto*/
static void (*__pyx_f_8obitools_5align_8_dynamic_reversePath)(struct __pyx_t_8obitools_5align_8_dynamic_alignPath *); /*proto*/
static void (*__pyx_f_8obitools_5align_8_dynamic_freePath)(struct __pyx_t_8obitools_5align_8_dynamic_alignPath *); /*proto*/
static int (*__pyx_f_8obitools_5align_8_dynamic_bitCount)(int); /*proto*/
static int (*__pyx_f_8obitools_5align_8_dynamic_iupacMatch)(unsigned char, unsigned char, int __pyx_skip_dispatch); /*proto*/
static double (*__pyx_f_8obitools_5align_8_dynamic_iupacPartialMatch)(unsigned char, unsigned char, int __pyx_skip_dispatch); /*proto*/
@@ -513,8 +553,6 @@ static char __pyx_k___main__[] = "__main__";
static PyObject *__pyx_kp___main__;
static char __pyx_k___init__[] = "__init__";
static PyObject *__pyx_kp___init__;
static char __pyx_k_backtrack[] = "backtrack";
static PyObject *__pyx_kp_backtrack;
static char __pyx_k_opengap[] = "opengap";
static PyObject *__pyx_kp_opengap;
static char __pyx_k_extgap[] = "extgap";
@@ -632,7 +670,6 @@ static double __pyx_f_8obitools_5align_4_lcs_3LCS_doAlignment(struct __pyx_obj_
int __pyx_t_2;
int __pyx_t_3;
int __pyx_t_4;
PyObject *__pyx_t_5 = NULL;
__Pyx_SetupRefcountContext("doAlignment");
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":31
@@ -683,10 +720,7 @@ static double __pyx_f_8obitools_5align_4_lcs_3LCS_doAlignment(struct __pyx_obj_
* self.matrix.matrix[idx].score = 0
* self.matrix.matrix[idx].path = j
*/
__pyx_t_1 = PyInt_FromLong(__pyx_v_j); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_lcs_LCS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_t_1, __pyx_int_0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_lcs_LCS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_v_j, 0);
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":37
* for j in range(1,self.hSeq.length+1):
@@ -724,10 +758,7 @@ static double __pyx_f_8obitools_5align_4_lcs_3LCS_doAlignment(struct __pyx_obj_
* self.matrix.matrix[idx].score = 0
* self.matrix.matrix[idx].path = -i
*/
__pyx_t_1 = PyInt_FromLong(__pyx_v_i); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_lcs_LCS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_int_0, __pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_lcs_LCS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), 0, __pyx_v_i);
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":42
* for i in range(1,self.vSeq.length+1):
@@ -775,13 +806,7 @@ static double __pyx_f_8obitools_5align_4_lcs_3LCS_doAlignment(struct __pyx_obj_
* # print "computing cell : %d,%d --> %d/%d" % (j,i,self.index(j,i),self.matrix.msize),
* scoremax = self.matrix.matrix[idx].score + \
*/
__pyx_t_1 = PyInt_FromLong((__pyx_v_j - 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_5 = PyInt_FromLong((__pyx_v_i - 1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_lcs_LCS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_t_1, __pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_lcs_LCS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), (__pyx_v_j - 1), (__pyx_v_i - 1));
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":52
* # print "computing cell : %d,%d --> %d/%d" % (j,i,self.index(j,i),self.matrix.msize),
@@ -808,13 +833,7 @@ static double __pyx_f_8obitools_5align_4_lcs_3LCS_doAlignment(struct __pyx_obj_
* score = self.matrix.matrix[idx].score
* if score > scoremax :
*/
__pyx_t_5 = PyInt_FromLong((__pyx_v_j - 1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_1 = PyInt_FromLong(__pyx_v_i); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_lcs_LCS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_t_5, __pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_lcs_LCS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), (__pyx_v_j - 1), __pyx_v_i);
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":59
* # 2 - open horizontal gap
@@ -896,13 +915,7 @@ static double __pyx_f_8obitools_5align_4_lcs_3LCS_doAlignment(struct __pyx_obj_
* score = self.matrix.matrix[idx].score
* if score > scoremax :
*/
__pyx_t_1 = PyInt_FromLong(__pyx_v_j); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_5 = PyInt_FromLong((__pyx_v_i - 1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_lcs_LCS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_t_1, __pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":70
* # 3 - open vertical gap
@@ -984,13 +997,7 @@ static double __pyx_f_8obitools_5align_4_lcs_3LCS_doAlignment(struct __pyx_obj_
* self.matrix.matrix[idx].score = scoremax
* self.matrix.matrix[idx].path = path
*/
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__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_lcs_LCS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_t_5, __pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":80
*
@@ -1040,20 +1047,14 @@ static double __pyx_f_8obitools_5align_4_lcs_3LCS_doAlignment(struct __pyx_obj_
* return self.matrix.matrix[idx].score
*
*/
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__Pyx_GOTREF(__pyx_t_5);
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_lcs_LCS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_t_1, __pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_lcs_LCS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_v_self->__pyx_base.hSeq->length, __pyx_v_self->__pyx_base.vSeq->length);
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":87
*
* idx = self.index(self.hSeq.length,self.vSeq.length)
* return self.matrix.matrix[idx].score # <<<<<<<<<<<<<<
*
* def backtrack(self):
* cdef void backtrack(self):
*/
__pyx_r = (__pyx_v_self->__pyx_base.matrix->matrix[__pyx_v_idx]).score;
goto __pyx_L0;
@@ -1062,7 +1063,6 @@ static double __pyx_f_8obitools_5align_4_lcs_3LCS_doAlignment(struct __pyx_obj_
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_5);
__Pyx_AddTraceback("obitools.align._lcs.LCS.doAlignment");
__pyx_r = 0;
__pyx_L0:;
@@ -1073,37 +1073,21 @@ static double __pyx_f_8obitools_5align_4_lcs_3LCS_doAlignment(struct __pyx_obj_
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":89
* return self.matrix.matrix[idx].score
*
* def backtrack(self): # <<<<<<<<<<<<<<
* cdef list path=[]
* cdef void backtrack(self): # <<<<<<<<<<<<<<
* #cdef list path=[]
* cdef int i
*/
static PyObject *__pyx_pf_8obitools_5align_4_lcs_3LCS_backtrack(PyObject *__pyx_v_self, PyObject *unused); /*proto*/
static PyObject *__pyx_pf_8obitools_5align_4_lcs_3LCS_backtrack(PyObject *__pyx_v_self, PyObject *unused) {
PyObject *__pyx_v_path = 0;
static void __pyx_f_8obitools_5align_4_lcs_3LCS_backtrack(struct __pyx_obj_8obitools_5align_4_lcs_LCS *__pyx_v_self) {
int __pyx_v_i;
int __pyx_v_j;
int __pyx_v_p;
PyObject *__pyx_r = NULL;
PyObject *__pyx_t_1 = NULL;
double __pyx_t_2;
struct __pyx_opt_args_8obitools_5align_8_dynamic_allocatePath __pyx_1;
double __pyx_t_1;
struct __pyx_t_8obitools_5align_8_dynamic_alignPath *__pyx_t_2;
int __pyx_t_3;
PyObject *__pyx_t_4 = NULL;
int __pyx_t_5;
__Pyx_SetupRefcountContext("backtrack");
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":90
*
* def backtrack(self):
* cdef list path=[] # <<<<<<<<<<<<<<
* cdef int i
* cdef int j
*/
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_v_path = __pyx_t_1;
__pyx_t_1 = 0;
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":95
* cdef int p
*
@@ -1111,32 +1095,44 @@ static PyObject *__pyx_pf_8obitools_5align_4_lcs_3LCS_backtrack(PyObject *__pyx_
* i=self.vSeq.length
* j=self.hSeq.length
*/
__pyx_t_2 = ((struct __pyx_vtabstruct_8obitools_5align_4_lcs_LCS *)((struct __pyx_obj_8obitools_5align_4_lcs_LCS *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.doAlignment(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self)); if (unlikely(__pyx_t_2 == 0 && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_1 = ((struct __pyx_vtabstruct_8obitools_5align_4_lcs_LCS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.doAlignment(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self)); if (unlikely(__pyx_t_1 == 0 && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":96
*
* self.doAlignment()
* i=self.vSeq.length # <<<<<<<<<<<<<<
* j=self.hSeq.length
*
* self.path=allocatePath(i,j,self.path)
*/
__pyx_v_i = ((struct __pyx_obj_8obitools_5align_4_lcs_LCS *)__pyx_v_self)->__pyx_base.vSeq->length;
__pyx_v_i = __pyx_v_self->__pyx_base.vSeq->length;
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":97
* self.doAlignment()
* i=self.vSeq.length
* j=self.hSeq.length # <<<<<<<<<<<<<<
* self.path=allocatePath(i,j,self.path)
*
*/
__pyx_v_j = __pyx_v_self->__pyx_base.hSeq->length;
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":98
* i=self.vSeq.length
* j=self.hSeq.length
* self.path=allocatePath(i,j,self.path) # <<<<<<<<<<<<<<
*
* while (i or j):
*/
__pyx_v_j = ((struct __pyx_obj_8obitools_5align_4_lcs_LCS *)__pyx_v_self)->__pyx_base.hSeq->length;
__pyx_1.__pyx_n = 1;
__pyx_1.path = __pyx_v_self->__pyx_base.path;
__pyx_t_2 = __pyx_f_8obitools_5align_8_dynamic_allocatePath(__pyx_v_i, __pyx_v_j, &__pyx_1);
__pyx_v_self->__pyx_base.path = __pyx_t_2;
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":99
* j=self.hSeq.length
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":100
* self.path=allocatePath(i,j,self.path)
*
* while (i or j): # <<<<<<<<<<<<<<
* p=self.matrix.matrix[self.index(j,i)].path
* path.append(p)
* self.path.path[self.path.length]=p
*/
while (1) {
if (!__pyx_v_i) {
@@ -1146,36 +1142,36 @@ static PyObject *__pyx_pf_8obitools_5align_4_lcs_3LCS_backtrack(PyObject *__pyx_
}
if (!__pyx_t_3) break;
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":100
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":101
*
* while (i or j):
* p=self.matrix.matrix[self.index(j,i)].path # <<<<<<<<<<<<<<
* path.append(p)
* if p==0:
* self.path.path[self.path.length]=p
* self.path.length+=1
*/
__pyx_t_1 = PyInt_FromLong(__pyx_v_j); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 100; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":101
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* i-=1
*/
__pyx_t_4 = PyInt_FromLong(__pyx_v_p); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":102
* while (i or j):
* p=self.matrix.matrix[self.index(j,i)].path
* path.append(p)
* self.path.path[self.path.length]=p # <<<<<<<<<<<<<<
* self.path.length+=1
* # path.append(p)
*/
(__pyx_v_self->__pyx_base.path->path[__pyx_v_self->__pyx_base.path->length]) = __pyx_v_p;
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":103
* p=self.matrix.matrix[self.index(j,i)].path
* self.path.path[self.path.length]=p
* self.path.length+=1 # <<<<<<<<<<<<<<
* # path.append(p)
* if p==0:
*/
__pyx_v_self->__pyx_base.path->length += 1;
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":105
* self.path.length+=1
* # path.append(p)
* if p==0: # <<<<<<<<<<<<<<
* i-=1
* j-=1
@@ -1183,8 +1179,8 @@ static PyObject *__pyx_pf_8obitools_5align_4_lcs_3LCS_backtrack(PyObject *__pyx_
__pyx_t_3 = (__pyx_v_p == 0);
if (__pyx_t_3) {
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":103
* path.append(p)
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":106
* # path.append(p)
* if p==0:
* i-=1 # <<<<<<<<<<<<<<
* j-=1
@@ -1192,7 +1188,7 @@ static PyObject *__pyx_pf_8obitools_5align_4_lcs_3LCS_backtrack(PyObject *__pyx_
*/
__pyx_v_i -= 1;
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":104
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":107
* if p==0:
* i-=1
* j-=1 # <<<<<<<<<<<<<<
@@ -1200,10 +1196,10 @@ static PyObject *__pyx_pf_8obitools_5align_4_lcs_3LCS_backtrack(PyObject *__pyx_
* i+=p
*/
__pyx_v_j -= 1;
goto __pyx_L7;
goto __pyx_L5;
}
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":105
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":108
* i-=1
* j-=1
* elif p < 0: # <<<<<<<<<<<<<<
@@ -1213,7 +1209,7 @@ static PyObject *__pyx_pf_8obitools_5align_4_lcs_3LCS_backtrack(PyObject *__pyx_
__pyx_t_3 = (__pyx_v_p < 0);
if (__pyx_t_3) {
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":106
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":109
* j-=1
* elif p < 0:
* i+=p # <<<<<<<<<<<<<<
@@ -1221,66 +1217,45 @@ static PyObject *__pyx_pf_8obitools_5align_4_lcs_3LCS_backtrack(PyObject *__pyx_
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*/
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goto __pyx_L7;
goto __pyx_L5;
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/*else*/ {
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":108
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":111
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* path.reverse()
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__pyx_L7:;
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":110
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*
* path.reverse() # <<<<<<<<<<<<<<
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":115
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":116
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__pyx_t_5 = PyList_Reverse(((PyObject *)__pyx_v_path)); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_self->__pyx_base.path->vStart = 0;
/* "/Users/coissac/encours/OBITools/src/obitools/align/_lcs.pyx":111
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goto __pyx_L0;
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goto __pyx_L0;
__pyx_L1_error:;
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static struct __pyx_vtabstruct_8obitools_5align_4_lcs_LCS __pyx_vtable_8obitools_5align_4_lcs_LCS;
@@ -1313,7 +1288,6 @@ static int __pyx_tp_clear_8obitools_5align_4_lcs_LCS(PyObject *o) {
}
static struct PyMethodDef __pyx_methods_8obitools_5align_4_lcs_LCS[] = {
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{0, 0, 0, 0}
};
@@ -1486,7 +1460,6 @@ static struct PyModuleDef __pyx_moduledef = {
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{&__pyx_kp_backtrack, __pyx_k_backtrack, sizeof(__pyx_k_backtrack), 1, 1, 1},
{&__pyx_kp_opengap, __pyx_k_opengap, sizeof(__pyx_k_opengap), 1, 1, 1},
{&__pyx_kp_extgap, __pyx_k_extgap, sizeof(__pyx_k_extgap), 1, 1, 1},
{&__pyx_kp_needToCompute, __pyx_k_needToCompute, sizeof(__pyx_k_needToCompute), 1, 1, 1},
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#if PY_MAJOR_VERSION >= 3
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__pyx_vtable_8obitools_5align_4_lcs_LCS.__pyx_base.doAlignment = (double (*)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *))__pyx_f_8obitools_5align_4_lcs_3LCS_doAlignment;
__pyx_vtable_8obitools_5align_4_lcs_LCS.__pyx_base.backtrack = (void (*)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *))__pyx_f_8obitools_5align_4_lcs_3LCS_backtrack;
#else
*(void(**)(void))&__pyx_vtable_8obitools_5align_4_lcs_LCS.__pyx_base.matchScore = (void(*)(void))__pyx_f_8obitools_5align_4_lcs_3LCS_matchScore;
*(void(**)(void))&__pyx_vtable_8obitools_5align_4_lcs_LCS.__pyx_base.doAlignment = (void(*)(void))__pyx_f_8obitools_5align_4_lcs_3LCS_doAlignment;
*(void(**)(void))&__pyx_vtable_8obitools_5align_4_lcs_LCS.__pyx_base.backtrack = (void(*)(void))__pyx_f_8obitools_5align_4_lcs_3LCS_backtrack;
#endif
__pyx_type_8obitools_5align_4_lcs_LCS.tp_base = __pyx_ptype_8obitools_5align_8_dynamic_DynamicProgramming;
if (PyType_Ready(&__pyx_type_8obitools_5align_4_lcs_LCS) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -1591,6 +1566,9 @@ PyMODINIT_FUNC PyInit__lcs(void)
if (__Pyx_ImportFunction(__pyx_1, "resetMatrix", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_resetMatrix, "void (struct __pyx_t_8obitools_5align_8_dynamic_AlignMatrix *)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_ImportFunction(__pyx_1, "allocateSequence", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_allocateSequence, "struct __pyx_t_8obitools_5align_8_dynamic_alignSequence *(PyObject *, struct __pyx_opt_args_8obitools_5align_8_dynamic_allocateSequence *__pyx_optional_args)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_ImportFunction(__pyx_1, "freeSequence", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_freeSequence, "void (struct __pyx_t_8obitools_5align_8_dynamic_alignSequence *)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_ImportFunction(__pyx_1, "allocatePath", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_allocatePath, "struct __pyx_t_8obitools_5align_8_dynamic_alignPath *(long, long, struct __pyx_opt_args_8obitools_5align_8_dynamic_allocatePath *__pyx_optional_args)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_ImportFunction(__pyx_1, "reversePath", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_reversePath, "void (struct __pyx_t_8obitools_5align_8_dynamic_alignPath *)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_ImportFunction(__pyx_1, "freePath", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_freePath, "void (struct __pyx_t_8obitools_5align_8_dynamic_alignPath *)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_ImportFunction(__pyx_1, "bitCount", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_bitCount, "int (int)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_ImportFunction(__pyx_1, "iupacMatch", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_iupacMatch, "int (unsigned char, unsigned char, int __pyx_skip_dispatch)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_ImportFunction(__pyx_1, "iupacPartialMatch", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_iupacPartialMatch, "double (unsigned char, unsigned char, int __pyx_skip_dispatch)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -2041,6 +2019,68 @@ static INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
}
}
static INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
#if PY_MAJOR_VERSION >= 3
/* Note: this is a temporary work-around to prevent crashes in Python 3.0 */
if ((tstate->exc_type != NULL) & (tstate->exc_type != Py_None)) {
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
tmp_tb = tstate->exc_traceback;
PyErr_NormalizeException(&type, &value, &tb);
PyErr_NormalizeException(&tmp_type, &tmp_value, &tmp_tb);
tstate->exc_type = 0;
tstate->exc_value = 0;
tstate->exc_traceback = 0;
PyException_SetContext(value, tmp_value);
Py_DECREF(tmp_type);
Py_XDECREF(tmp_tb);
}
#endif
tmp_type = tstate->curexc_type;
tmp_value = tstate->curexc_value;
tmp_tb = tstate->curexc_traceback;
tstate->curexc_type = type;
tstate->curexc_value = value;
tstate->curexc_traceback = tb;
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
}
static INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->curexc_type;
*value = tstate->curexc_value;
*tb = tstate->curexc_traceback;
tstate->curexc_type = 0;
tstate->curexc_value = 0;
tstate->curexc_traceback = 0;
}
static void __Pyx_WriteUnraisable(const char *name) {
PyObject *old_exc, *old_val, *old_tb;
PyObject *ctx;
__Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
#if PY_MAJOR_VERSION < 3
ctx = PyString_FromString(name);
#else
ctx = PyUnicode_FromString(name);
#endif
__Pyx_ErrRestore(old_exc, old_val, old_tb);
if (!ctx) {
PyErr_WriteUnraisable(Py_None);
} else {
PyErr_WriteUnraisable(ctx);
Py_DECREF(ctx);
}
}
#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,

16
src/obitools/align/_lcs.pyx
View File

@@ -86,8 +86,8 @@ cdef class LCS(DynamicProgramming):
idx = self.index(self.hSeq.length,self.vSeq.length)
return self.matrix.matrix[idx].score
def backtrack(self):
cdef list path=[]
cdef void backtrack(self):
#cdef list path=[]
cdef int i
cdef int j
cdef int p
@@ -95,10 +95,13 @@ cdef class LCS(DynamicProgramming):
self.doAlignment()
i=self.vSeq.length
j=self.hSeq.length
self.path=allocatePath(i,j,self.path)
while (i or j):
p=self.matrix.matrix[self.index(j,i)].path
path.append(p)
self.path.path[self.path.length]=p
self.path.length+=1
# path.append(p)
if p==0:
i-=1
j-=1
@@ -107,8 +110,11 @@ cdef class LCS(DynamicProgramming):
else:
j-=p
path.reverse()
return 0,0,path
#path.reverse()
#reversePath(self.path)
self.path.hStart=0
self.path.vStart=0
#return 0,0,path

386
src/obitools/align/_nws.c
View File

@@ -1,4 +1,4 @@
/* Generated by Cython 0.11.3 on Sun Nov 8 08:26:04 2009 */
/* Generated by Cython 0.11.3 on Mon Jan 4 22:18:11 2010 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -337,6 +337,11 @@ static INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *);
static INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *);
static INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
static INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
static void __Pyx_WriteUnraisable(const char *name); /*proto*/
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, long size); /*proto*/
static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
@@ -425,7 +430,36 @@ struct __pyx_opt_args_8obitools_5align_8_dynamic_allocateSequence {
struct __pyx_t_8obitools_5align_8_dynamic_alignSequence *seq;
};
/* "/Users/coissac/encours/OBITools/src/obitools/align/_dynamic.pxd":47
/* "/Users/coissac/encours/OBITools/src/obitools/align/_dynamic.pxd":42
* cdef void freeSequence(alignSequence* seq)
*
* cdef struct alignPath: # <<<<<<<<<<<<<<
* long length
* long buffsize
*/
struct __pyx_t_8obitools_5align_8_dynamic_alignPath {
long length;
long buffsize;
long vStart;
long hStart;
long *path;
};
/* "/Users/coissac/encours/OBITools/src/obitools/align/_dynamic.pxd":49
* long *path
*
* cdef alignPath* allocatePath(long l1,long l2,alignPath* path=?) # <<<<<<<<<<<<<<
*
* cdef void reversePath(alignPath* path)
*/
struct __pyx_opt_args_8obitools_5align_8_dynamic_allocatePath {
int __pyx_n;
struct __pyx_t_8obitools_5align_8_dynamic_alignPath *path;
};
/* "/Users/coissac/encours/OBITools/src/obitools/align/_dynamic.pxd":61
* cpdef double iupacPartialMatch(unsigned char a, unsigned char b)
*
* cdef class DynamicProgramming: # <<<<<<<<<<<<<<
@@ -441,6 +475,7 @@ struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming {
PyObject *verticalSeq;
struct __pyx_t_8obitools_5align_8_dynamic_alignSequence *hSeq;
struct __pyx_t_8obitools_5align_8_dynamic_alignSequence *vSeq;
struct __pyx_t_8obitools_5align_8_dynamic_alignPath *path;
double _opengap;
double _extgap;
PyObject *alignment;
@@ -463,7 +498,7 @@ struct __pyx_obj_8obitools_5align_4_nws_NWS {
};
/* "/Users/coissac/encours/OBITools/src/obitools/align/_dynamic.pxd":47
/* "/Users/coissac/encours/OBITools/src/obitools/align/_dynamic.pxd":61
* cpdef double iupacPartialMatch(unsigned char a, unsigned char b)
*
* cdef class DynamicProgramming: # <<<<<<<<<<<<<<
@@ -476,7 +511,9 @@ struct __pyx_vtabstruct_8obitools_5align_8_dynamic_DynamicProgramming {
double (*matchScore)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *, int, int);
double (*doAlignment)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *);
void (*reset)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *);
int (*index)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *, PyObject *, PyObject *);
int (*index)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *, int, int);
int (*_needToCompute)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *);
void (*backtrack)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *);
};
static struct __pyx_vtabstruct_8obitools_5align_8_dynamic_DynamicProgramming *__pyx_vtabptr_8obitools_5align_8_dynamic_DynamicProgramming;
@@ -501,6 +538,9 @@ static void (*__pyx_f_8obitools_5align_8_dynamic_freeMatrix)(struct __pyx_t_8obi
static void (*__pyx_f_8obitools_5align_8_dynamic_resetMatrix)(struct __pyx_t_8obitools_5align_8_dynamic_AlignMatrix *); /*proto*/
static struct __pyx_t_8obitools_5align_8_dynamic_alignSequence *(*__pyx_f_8obitools_5align_8_dynamic_allocateSequence)(PyObject *, struct __pyx_opt_args_8obitools_5align_8_dynamic_allocateSequence *__pyx_optional_args); /*proto*/
static void (*__pyx_f_8obitools_5align_8_dynamic_freeSequence)(struct __pyx_t_8obitools_5align_8_dynamic_alignSequence *); /*proto*/
static struct __pyx_t_8obitools_5align_8_dynamic_alignPath *(*__pyx_f_8obitools_5align_8_dynamic_allocatePath)(long, long, struct __pyx_opt_args_8obitools_5align_8_dynamic_allocatePath *__pyx_optional_args); /*proto*/
static void (*__pyx_f_8obitools_5align_8_dynamic_reversePath)(struct __pyx_t_8obitools_5align_8_dynamic_alignPath *); /*proto*/
static void (*__pyx_f_8obitools_5align_8_dynamic_freePath)(struct __pyx_t_8obitools_5align_8_dynamic_alignPath *); /*proto*/
static int (*__pyx_f_8obitools_5align_8_dynamic_bitCount)(int); /*proto*/
static int (*__pyx_f_8obitools_5align_8_dynamic_iupacMatch)(unsigned char, unsigned char, int __pyx_skip_dispatch); /*proto*/
static double (*__pyx_f_8obitools_5align_8_dynamic_iupacPartialMatch)(unsigned char, unsigned char, int __pyx_skip_dispatch); /*proto*/
@@ -516,13 +556,10 @@ static PyObject *__pyx_int_neg_6;
static PyObject *__pyx_int_neg_8;
static PyObject *__pyx_int_neg_2;
static PyObject *__pyx_int_1;
static PyObject *__pyx_int_0;
static char __pyx_k___main__[] = "__main__";
static PyObject *__pyx_kp___main__;
static char __pyx_k___init__[] = "__init__";
static PyObject *__pyx_kp___init__;
static char __pyx_k_backtrack[] = "backtrack";
static PyObject *__pyx_kp_backtrack;
static char __pyx_k_match[] = "match";
static PyObject *__pyx_kp_match;
static char __pyx_k_mismatch[] = "mismatch";
@@ -743,7 +780,6 @@ static double __pyx_f_8obitools_5align_4_nws_3NWS_doAlignment(struct __pyx_obj_
int __pyx_t_2;
int __pyx_t_3;
int __pyx_t_4;
PyObject *__pyx_t_5 = NULL;
__Pyx_SetupRefcountContext("doAlignment");
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":34
@@ -794,10 +830,7 @@ static double __pyx_f_8obitools_5align_4_nws_3NWS_doAlignment(struct __pyx_obj_
* self.matrix.matrix[idx].score = self._opengap + (self._extgap * (j-1))
* self.matrix.matrix[idx].path = j
*/
__pyx_t_1 = PyInt_FromLong(__pyx_v_j); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_nws_NWS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_t_1, __pyx_int_0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_nws_NWS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_v_j, 0);
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":40
* for j in range(1,self.hSeq.length+1):
@@ -835,10 +868,7 @@ static double __pyx_f_8obitools_5align_4_nws_3NWS_doAlignment(struct __pyx_obj_
* self.matrix.matrix[idx].score = self._opengap + (self._extgap * (i-1))
* self.matrix.matrix[idx].path = -i
*/
__pyx_t_1 = PyInt_FromLong(__pyx_v_i); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_nws_NWS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_int_0, __pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_nws_NWS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), 0, __pyx_v_i);
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":45
* for i in range(1,self.vSeq.length+1):
@@ -886,13 +916,7 @@ static double __pyx_f_8obitools_5align_4_nws_3NWS_doAlignment(struct __pyx_obj_
* # print "computing cell : %d,%d --> %d/%d" % (j,i,self.index(j,i),self.matrix.msize),
* scoremax = self.matrix.matrix[idx].score + \
*/
__pyx_t_1 = PyInt_FromLong((__pyx_v_j - 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_5 = PyInt_FromLong((__pyx_v_i - 1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_nws_NWS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_t_1, __pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_nws_NWS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), (__pyx_v_j - 1), (__pyx_v_i - 1));
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":55
* # print "computing cell : %d,%d --> %d/%d" % (j,i,self.index(j,i),self.matrix.msize),
@@ -919,13 +943,7 @@ static double __pyx_f_8obitools_5align_4_nws_3NWS_doAlignment(struct __pyx_obj_
* score = self.matrix.matrix[idx].score + \
* self._opengap
*/
__pyx_t_5 = PyInt_FromLong((__pyx_v_j - 1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_1 = PyInt_FromLong(__pyx_v_i); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_nws_NWS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_t_5, __pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_nws_NWS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), (__pyx_v_j - 1), __pyx_v_i);
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":63
* idx = self.index(j-1,i)
@@ -974,13 +992,7 @@ static double __pyx_f_8obitools_5align_4_nws_3NWS_doAlignment(struct __pyx_obj_
* score = self.matrix.matrix[idx].score + \
* self._opengap
*/
__pyx_t_1 = PyInt_FromLong(__pyx_v_j); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_5 = PyInt_FromLong((__pyx_v_i - 1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_nws_NWS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_t_1, __pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_nws_NWS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_v_j, (__pyx_v_i - 1));
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":71
* idx = self.index(j,i-1)
@@ -1048,13 +1060,7 @@ static double __pyx_f_8obitools_5align_4_nws_3NWS_doAlignment(struct __pyx_obj_
* delta = j-jump
* score = self.matrix.matrix[idx].score + \
*/
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":80
* if jump >= 0:
@@ -1134,13 +1140,7 @@ static double __pyx_f_8obitools_5align_4_nws_3NWS_doAlignment(struct __pyx_obj_
* delta = i-jump
* score = self.matrix.matrix[idx].score + \
*/
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":91
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@@ -1201,13 +1201,7 @@ static double __pyx_f_8obitools_5align_4_nws_3NWS_doAlignment(struct __pyx_obj_
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__pyx_v_idx = ((struct __pyx_vtabstruct_8obitools_5align_4_nws_NWS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.index(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self), __pyx_t_5, __pyx_t_1);
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":99
*
@@ -1300,20 +1294,14 @@ static double __pyx_f_8obitools_5align_4_nws_3NWS_doAlignment(struct __pyx_obj_
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*
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":111
*
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*
* def backtrack(self):
* cdef void backtrack(self):
*/
__pyx_r = (__pyx_v_self->__pyx_base.matrix->matrix[__pyx_v_idx]).score;
goto __pyx_L0;
@@ -1322,7 +1310,6 @@ static double __pyx_f_8obitools_5align_4_nws_3NWS_doAlignment(struct __pyx_obj_
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_5);
__Pyx_AddTraceback("obitools.align._nws.NWS.doAlignment");
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__pyx_L0:;
@@ -1333,37 +1320,21 @@ static double __pyx_f_8obitools_5align_4_nws_3NWS_doAlignment(struct __pyx_obj_
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":113
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* def backtrack(self): # <<<<<<<<<<<<<<
* cdef list path=[]
* cdef void backtrack(self): # <<<<<<<<<<<<<<
* #cdef list path=[]
* cdef int i
*/
static PyObject *__pyx_pf_8obitools_5align_4_nws_3NWS_backtrack(PyObject *__pyx_v_self, PyObject *unused); /*proto*/
static PyObject *__pyx_pf_8obitools_5align_4_nws_3NWS_backtrack(PyObject *__pyx_v_self, PyObject *unused) {
PyObject *__pyx_v_path = 0;
static void __pyx_f_8obitools_5align_4_nws_3NWS_backtrack(struct __pyx_obj_8obitools_5align_4_nws_NWS *__pyx_v_self) {
int __pyx_v_i;
int __pyx_v_j;
int __pyx_v_p;
PyObject *__pyx_r = NULL;
PyObject *__pyx_t_1 = NULL;
double __pyx_t_2;
struct __pyx_opt_args_8obitools_5align_8_dynamic_allocatePath __pyx_1;
double __pyx_t_1;
struct __pyx_t_8obitools_5align_8_dynamic_alignPath *__pyx_t_2;
int __pyx_t_3;
PyObject *__pyx_t_4 = NULL;
int __pyx_t_5;
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":114
*
* def backtrack(self):
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* cdef int i
* cdef int j
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__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_v_path = __pyx_t_1;
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":119
* cdef int p
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@@ -1371,32 +1342,44 @@ static PyObject *__pyx_pf_8obitools_5align_4_nws_3NWS_backtrack(PyObject *__pyx_
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__pyx_t_1 = ((struct __pyx_vtabstruct_8obitools_5align_4_nws_NWS *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.doAlignment(((struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *)__pyx_v_self)); if (unlikely(__pyx_t_1 == 0 && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":120
*
* self.doAlignment()
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* j=self.hSeq.length
*
* self.path=allocatePath(i,j,self.path)
*/
__pyx_v_i = ((struct __pyx_obj_8obitools_5align_4_nws_NWS *)__pyx_v_self)->__pyx_base.vSeq->length;
__pyx_v_i = __pyx_v_self->__pyx_base.vSeq->length;
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":121
* self.doAlignment()
* i=self.vSeq.length
* j=self.hSeq.length # <<<<<<<<<<<<<<
* self.path=allocatePath(i,j,self.path)
*
*/
__pyx_v_j = __pyx_v_self->__pyx_base.hSeq->length;
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":122
* i=self.vSeq.length
* j=self.hSeq.length
* self.path=allocatePath(i,j,self.path) # <<<<<<<<<<<<<<
*
* while (i or j):
*/
__pyx_v_j = ((struct __pyx_obj_8obitools_5align_4_nws_NWS *)__pyx_v_self)->__pyx_base.hSeq->length;
__pyx_1.__pyx_n = 1;
__pyx_1.path = __pyx_v_self->__pyx_base.path;
__pyx_t_2 = __pyx_f_8obitools_5align_8_dynamic_allocatePath(__pyx_v_i, __pyx_v_j, &__pyx_1);
__pyx_v_self->__pyx_base.path = __pyx_t_2;
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":123
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":124
* self.path=allocatePath(i,j,self.path)
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@@ -1406,36 +1389,36 @@ static PyObject *__pyx_pf_8obitools_5align_4_nws_3NWS_backtrack(PyObject *__pyx_
}
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":124
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":125
*
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* path.append(p)
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*/
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":125
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":126
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":127
* p=self.matrix.matrix[self.index(j,i)].path
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*/
__pyx_v_self->__pyx_base.path->length += 1;
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":129
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":127
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":128
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":131
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* i-=1
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goto __pyx_L7;
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":129
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":132
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":130
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":132
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":135
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/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":138
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PyObject *__pyx_t_1 = NULL;
__Pyx_SetupRefcountContext("__get__");
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":139
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":146
* property match:
* def __get__(self):
* return self._match # <<<<<<<<<<<<<<
@@ -1565,7 +1527,7 @@ static PyObject *__pyx_pf_8obitools_5align_4_nws_3NWS_5match___get__(PyObject *_
* def __set__(self,match):
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_1 = PyFloat_FromDouble(((struct __pyx_obj_8obitools_5align_4_nws_NWS *)__pyx_v_self)->_match); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_1 = PyFloat_FromDouble(((struct __pyx_obj_8obitools_5align_4_nws_NWS *)__pyx_v_self)->_match); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 146; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -1583,7 +1545,7 @@ static PyObject *__pyx_pf_8obitools_5align_4_nws_3NWS_5match___get__(PyObject *_
return __pyx_r;
}
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":141
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":148
* return self._match
*
* def __set__(self,match): # <<<<<<<<<<<<<<
@@ -1597,17 +1559,17 @@ static int __pyx_pf_8obitools_5align_4_nws_3NWS_5match___set__(PyObject *__pyx_v
double __pyx_t_1;
__Pyx_SetupRefcountContext("__set__");
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":142
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":149
*
* def __set__(self,match):
* self._match=match # <<<<<<<<<<<<<<
* self.scoreChanged=True
*
*/
__pyx_t_1 = __pyx_PyFloat_AsDouble(__pyx_v_match); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_1 = __pyx_PyFloat_AsDouble(__pyx_v_match); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
((struct __pyx_obj_8obitools_5align_4_nws_NWS *)__pyx_v_self)->_match = __pyx_t_1;
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":143
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":150
* def __set__(self,match):
* self._match=match
* self.scoreChanged=True # <<<<<<<<<<<<<<
@@ -1626,7 +1588,7 @@ static int __pyx_pf_8obitools_5align_4_nws_3NWS_5match___set__(PyObject *__pyx_v
return __pyx_r;
}
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":146
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":153
*
* property mismatch:
* def __get__(self): # <<<<<<<<<<<<<<
@@ -1640,7 +1602,7 @@ static PyObject *__pyx_pf_8obitools_5align_4_nws_3NWS_8mismatch___get__(PyObject
PyObject *__pyx_t_1 = NULL;
__Pyx_SetupRefcountContext("__get__");
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":147
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":154
* property mismatch:
* def __get__(self):
* return self._mismatch # <<<<<<<<<<<<<<
@@ -1648,7 +1610,7 @@ static PyObject *__pyx_pf_8obitools_5align_4_nws_3NWS_8mismatch___get__(PyObject
* def __set__(self,mismatch):
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_1 = PyFloat_FromDouble(((struct __pyx_obj_8obitools_5align_4_nws_NWS *)__pyx_v_self)->_mismatch); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 147; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_1 = PyFloat_FromDouble(((struct __pyx_obj_8obitools_5align_4_nws_NWS *)__pyx_v_self)->_mismatch); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -1666,7 +1628,7 @@ static PyObject *__pyx_pf_8obitools_5align_4_nws_3NWS_8mismatch___get__(PyObject
return __pyx_r;
}
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":149
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":156
* return self._mismatch
*
* def __set__(self,mismatch): # <<<<<<<<<<<<<<
@@ -1680,17 +1642,17 @@ static int __pyx_pf_8obitools_5align_4_nws_3NWS_8mismatch___set__(PyObject *__py
double __pyx_t_1;
__Pyx_SetupRefcountContext("__set__");
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":150
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":157
*
* def __set__(self,mismatch):
* self._mismatch=mismatch # <<<<<<<<<<<<<<
* self.scoreChanged=True
*
*/
__pyx_t_1 = __pyx_PyFloat_AsDouble(__pyx_v_mismatch); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_1 = __pyx_PyFloat_AsDouble(__pyx_v_mismatch); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
((struct __pyx_obj_8obitools_5align_4_nws_NWS *)__pyx_v_self)->_mismatch = __pyx_t_1;
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":151
/* "/Users/coissac/encours/OBITools/src/obitools/align/_nws.pyx":158
* def __set__(self,mismatch):
* self._mismatch=mismatch
* self.scoreChanged=True # <<<<<<<<<<<<<<
@@ -1767,7 +1729,6 @@ static int __pyx_setprop_8obitools_5align_4_nws_3NWS_mismatch(PyObject *o, PyObj
}
static struct PyMethodDef __pyx_methods_8obitools_5align_4_nws_NWS[] = {
{__Pyx_NAMESTR("backtrack"), (PyCFunction)__pyx_pf_8obitools_5align_4_nws_3NWS_backtrack, METH_NOARGS, __Pyx_DOCSTR(0)},
{0, 0, 0, 0}
};
@@ -1946,7 +1907,6 @@ static struct PyModuleDef __pyx_moduledef = {
static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_kp___main__, __pyx_k___main__, sizeof(__pyx_k___main__), 1, 1, 1},
{&__pyx_kp___init__, __pyx_k___init__, sizeof(__pyx_k___init__), 1, 1, 1},
{&__pyx_kp_backtrack, __pyx_k_backtrack, sizeof(__pyx_k_backtrack), 1, 1, 1},
{&__pyx_kp_match, __pyx_k_match, sizeof(__pyx_k_match), 1, 1, 1},
{&__pyx_kp_mismatch, __pyx_k_mismatch, sizeof(__pyx_k_mismatch), 1, 1, 1},
{&__pyx_kp_opengap, __pyx_k_opengap, sizeof(__pyx_k_opengap), 1, 1, 1},
@@ -1968,7 +1928,6 @@ static int __Pyx_InitGlobals(void) {
__pyx_int_neg_8 = PyInt_FromLong(-8); if (unlikely(!__pyx_int_neg_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__pyx_int_neg_2 = PyInt_FromLong(-2); if (unlikely(!__pyx_int_neg_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
__pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
return 0;
__pyx_L1_error:;
@@ -2040,9 +1999,11 @@ PyMODINIT_FUNC PyInit__nws(void)
#if PY_MAJOR_VERSION >= 3
__pyx_vtable_8obitools_5align_4_nws_NWS.__pyx_base.matchScore = (double (*)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *, int, int))__pyx_f_8obitools_5align_4_nws_3NWS_matchScore;
__pyx_vtable_8obitools_5align_4_nws_NWS.__pyx_base.doAlignment = (double (*)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *))__pyx_f_8obitools_5align_4_nws_3NWS_doAlignment;
__pyx_vtable_8obitools_5align_4_nws_NWS.__pyx_base.backtrack = (void (*)(struct __pyx_obj_8obitools_5align_8_dynamic_DynamicProgramming *))__pyx_f_8obitools_5align_4_nws_3NWS_backtrack;
#else
*(void(**)(void))&__pyx_vtable_8obitools_5align_4_nws_NWS.__pyx_base.matchScore = (void(*)(void))__pyx_f_8obitools_5align_4_nws_3NWS_matchScore;
*(void(**)(void))&__pyx_vtable_8obitools_5align_4_nws_NWS.__pyx_base.doAlignment = (void(*)(void))__pyx_f_8obitools_5align_4_nws_3NWS_doAlignment;
*(void(**)(void))&__pyx_vtable_8obitools_5align_4_nws_NWS.__pyx_base.backtrack = (void(*)(void))__pyx_f_8obitools_5align_4_nws_3NWS_backtrack;
#endif
__pyx_type_8obitools_5align_4_nws_NWS.tp_base = __pyx_ptype_8obitools_5align_8_dynamic_DynamicProgramming;
if (PyType_Ready(&__pyx_type_8obitools_5align_4_nws_NWS) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -2057,6 +2018,9 @@ PyMODINIT_FUNC PyInit__nws(void)
if (__Pyx_ImportFunction(__pyx_1, "resetMatrix", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_resetMatrix, "void (struct __pyx_t_8obitools_5align_8_dynamic_AlignMatrix *)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_ImportFunction(__pyx_1, "allocateSequence", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_allocateSequence, "struct __pyx_t_8obitools_5align_8_dynamic_alignSequence *(PyObject *, struct __pyx_opt_args_8obitools_5align_8_dynamic_allocateSequence *__pyx_optional_args)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_ImportFunction(__pyx_1, "freeSequence", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_freeSequence, "void (struct __pyx_t_8obitools_5align_8_dynamic_alignSequence *)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_ImportFunction(__pyx_1, "allocatePath", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_allocatePath, "struct __pyx_t_8obitools_5align_8_dynamic_alignPath *(long, long, struct __pyx_opt_args_8obitools_5align_8_dynamic_allocatePath *__pyx_optional_args)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_ImportFunction(__pyx_1, "reversePath", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_reversePath, "void (struct __pyx_t_8obitools_5align_8_dynamic_alignPath *)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_ImportFunction(__pyx_1, "freePath", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_freePath, "void (struct __pyx_t_8obitools_5align_8_dynamic_alignPath *)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_ImportFunction(__pyx_1, "bitCount", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_bitCount, "int (int)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_ImportFunction(__pyx_1, "iupacMatch", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_iupacMatch, "int (unsigned char, unsigned char, int __pyx_skip_dispatch)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_ImportFunction(__pyx_1, "iupacPartialMatch", (void (**)(void))&__pyx_f_8obitools_5align_8_dynamic_iupacPartialMatch, "double (unsigned char, unsigned char, int __pyx_skip_dispatch)") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -2565,6 +2529,68 @@ static INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) {
}
}
static INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
#if PY_MAJOR_VERSION >= 3
/* Note: this is a temporary work-around to prevent crashes in Python 3.0 */
if ((tstate->exc_type != NULL) & (tstate->exc_type != Py_None)) {
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
tmp_tb = tstate->exc_traceback;
PyErr_NormalizeException(&type, &value, &tb);
PyErr_NormalizeException(&tmp_type, &tmp_value, &tmp_tb);
tstate->exc_type = 0;
tstate->exc_value = 0;
tstate->exc_traceback = 0;
PyException_SetContext(value, tmp_value);
Py_DECREF(tmp_type);
Py_XDECREF(tmp_tb);
}
#endif
tmp_type = tstate->curexc_type;
tmp_value = tstate->curexc_value;
tmp_tb = tstate->curexc_traceback;
tstate->curexc_type = type;
tstate->curexc_value = value;
tstate->curexc_traceback = tb;
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
}
static INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->curexc_type;
*value = tstate->curexc_value;
*tb = tstate->curexc_traceback;
tstate->curexc_type = 0;
tstate->curexc_value = 0;
tstate->curexc_traceback = 0;
}
static void __Pyx_WriteUnraisable(const char *name) {
PyObject *old_exc, *old_val, *old_tb;
PyObject *ctx;
__Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
#if PY_MAJOR_VERSION < 3
ctx = PyString_FromString(name);
#else
ctx = PyUnicode_FromString(name);
#endif
__Pyx_ErrRestore(old_exc, old_val, old_tb);
if (!ctx) {
PyErr_WriteUnraisable(Py_None);
} else {
PyErr_WriteUnraisable(ctx);
Py_DECREF(ctx);
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#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,

3
src/obitools/align/_nws.pxd
View File

@@ -4,4 +4,7 @@ cdef class NWS(DynamicProgramming):
cdef double _match
cdef double _mismatch
cdef double matchScore(self,int h, int v)
cdef double doAlignment(self) except? 0

17
src/obitools/align/_nws.pyx
View File

@@ -110,8 +110,8 @@ cdef class NWS(DynamicProgramming):
idx = self.index(self.hSeq.length,self.vSeq.length)
return self.matrix.matrix[idx].score
def backtrack(self):
cdef list path=[]
cdef void backtrack(self):
#cdef list path=[]
cdef int i
cdef int j
cdef int p
@@ -119,10 +119,13 @@ cdef class NWS(DynamicProgramming):
self.doAlignment()
i=self.vSeq.length
j=self.hSeq.length
self.path=allocatePath(i,j,self.path)
while (i or j):
p=self.matrix.matrix[self.index(j,i)].path
path.append(p)
self.path.path[self.path.length]=p
self.path.length+=1
#path.append(p)
if p==0:
i-=1
j-=1
@@ -131,8 +134,12 @@ cdef class NWS(DynamicProgramming):
else:
j-=p
path.reverse()
return 0,0,path
#path.reverse()
#reversePath(self.path)
self.path.hStart=0
self.path.vStart=0
#return 0,0,path
property match:
def __get__(self):

2969
src/obitools/align/_qsassemble.c Normal file
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83
src/obitools/align/_qsassemble.pyx Normal file
View File

@@ -0,0 +1,83 @@
#@PydevCodeAnalysisIgnore
'''
Created on 6 Nov. 2009
@author: coissac
'''
from _dynamic cimport *
from _assemble cimport DirectAssemble
cdef class QSolexaDirectAssemble(DirectAssemble):
cdef double* hError
cdef double* vError
def __init__(self,match=4,opengap=-8,extgap=-2):
mismatch=-float(match)/3.0
DirectAssemble.__init__(self,match,mismatch,opengap,extgap)
cdef double matchScore(self,int h, int v):
cdef double score
cdef double smatch
cdef double smismatch
cdef double hok=1-self.hError[h-1]
cdef double vok=1-self.vError[v-1]
score=iupacPartialMatch(self.hSeq.sequence[h-1],self.vSeq.sequence[v-1])
smatch=((4*hok*vok-hok-vok)*(self._match-self._mismatch)+self._match+2*self._mismatch)/3
smismatch=((hok+vok-4*hok*vok)*(self._match-self._mismatch)+2*self._match+7*self._mismatch)/9
return smatch * score + smismatch * (1. - score)
property seqA:
def __get__(self):
return self.horizontalSeq
def __set__(self, seq):
cdef object oaddresse,olength
assert hasattr(seq, "quality"),"You must use sequence with quality indices"
self.sequenceChanged=True
self.horizontalSeq=seq
self.hSeq=allocateSequence(self.horizontalSeq,self.hSeq)
(oaddress,olength)=seq.quality.buffer_info()
self.hError=<double*><unsigned long int>oaddress
property seqB:
def __get__(self):
return self.verticalSeq
def __set__(self, seq):
cdef object oaddresse,olength
assert hasattr(seq, "quality"),"You must use sequence with quality indices"
self.sequenceChanged=True
self.verticalSeq=seq
self.vSeq=allocateSequence(self.verticalSeq,self.vSeq)
(oaddress,olength)=seq.quality.buffer_info()
self.vError=<double*><unsigned long int>oaddress
cdef class QSolexaReverseAssemble(QSolexaDirectAssemble):
cdef double matchScore(self,int h, int v):
cdef double score
cdef double smatch
cdef double smismatch
cdef double hok=1-self.hError[h-1]
cdef double vok=1-self.vError[self.vSeq.length - v]
score=iupacPartialMatch(self.hSeq.sequence[h-1],self.vSeq.sequence[v-1])
smatch=((4*hok*vok-hok-vok)*(self._match-self._mismatch)+self._match+2*self._mismatch)/3
smismatch=((hok+vok-4*hok*vok)*(self._match-self._mismatch)+2*self._match+7*self._mismatch)/9
return smatch * score + smismatch * (1. - score)
property seqB:
def __get__(self):
return self.verticalSeq.wrapped
def __set__(self, seq):
cdef object oaddresse,olength
assert hasattr(seq, "quality"),"You must use sequence with quality indices"
self.sequenceChanged=True
self.verticalSeq=seq.complement()
self.vSeq=allocateSequence(self.verticalSeq,self.vSeq)
(oaddress,olength)=seq.quality.buffer_info()
self.vError=<double*><unsigned long int>oaddress

2969
src/obitools/align/_qsrassemble.c Normal file
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3141
src/obitools/align/_rassemble.c Normal file
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File diff suppressed because it is too large Load Diff

10
src/obitools/align/_rassemble.pxd Normal file
View File

@@ -0,0 +1,10 @@
from _nws cimport *
cdef class RightDirectAssemble(NWS):
cdef double xsmax
cdef int xmax
cdef double doAlignment(self) except? 0
cdef class RightReverseAssemble(RightDirectAssemble):
pass

157
src/obitools/align/_rassemble.pyx Normal file
View File

@@ -0,0 +1,157 @@
#...@PydevCodeAnalysisIgnore
'''
Created on 6 Nov. 2009
@author: coissac
'''
from _rassemble cimport *
cdef class RightDirectAssemble(NWS):
def __init__(self,match=4,mismatch=-6,opengap=-8,extgap=-2):
NWS.__init__(self,match,mismatch,opengap,extgap)
self.xsmax=0
self.xmax=0
cdef double doAlignment(self) except? 0:
cdef int i # vertical index
cdef int j # horizontal index
cdef int idx
cdef int jump
cdef int delta
cdef double score
cdef double scoremax
cdef int path
if self.needToCompute:
self.allocate()
self.reset()
self.xsmax=0
self.xmax=0
for j in range(1,self.hSeq.length+1):
idx = self.index(j,0)
self.matrix.matrix[idx].score = self._opengap + (self._extgap * (j-1))
self.matrix.matrix[idx].path = j
for i in range(1,self.vSeq.length+1):
idx = self.index(0,i)
self.matrix.matrix[idx].score = 0
self.matrix.matrix[idx].path = -i
for i in range(1,self.vSeq.length+1):
for j in range(1,self.hSeq.length+1):
# 1 - came from diagonal
idx = self.index(j-1,i-1)
# print "computing cell : %d,%d --> %d/%d" % (j,i,self.index(j,i),self.matrix.msize),
scoremax = self.matrix.matrix[idx].score + \
self.matchScore(j,i)
path = 0
# print "so=%f sd=%f sm=%f" % (self.matrix.matrix[idx].score,self.matchScore(j,i),scoremax),
# 2 - open horizontal gap
idx = self.index(j-1,i)
score = self.matrix.matrix[idx].score+ \
self._opengap
if score > scoremax :
scoremax = score
path = +1
# 3 - open vertical gap
idx = self.index(j,i-1)
score = self.matrix.matrix[idx].score + \
self._opengap
if score > scoremax :
scoremax = score
path = -1
# 4 - extend horizontal gap
jump = self.matrix.bestHJump[i]
if jump >= 0:
idx = self.index(jump,i)
delta = j-jump
score = self.matrix.matrix[idx].score + \
self._extgap * delta
if score > scoremax :
scoremax = score
path = delta+1
# 5 - extend vertical gap
jump = self.matrix.bestVJump[j]
if jump >= 0:
idx = self.index(j,jump)
delta = i-jump
score = self.matrix.matrix[idx].score + \
self._extgap * delta
if score > scoremax :
scoremax = score
path = -delta-1
idx = self.index(j,i)
self.matrix.matrix[idx].score = scoremax
self.matrix.matrix[idx].path = path
if path == -1:
self.matrix.bestVJump[j]=i
elif path == +1 :
self.matrix.bestHJump[i]=j
if i==self.vSeq.length and scoremax > self.xsmax:
self.xsmax=scoremax
self.xmax=j
self.sequenceChanged=False
self.scoreChanged=False
return self.xsmax
cdef void backtrack(self):
cdef list path=[]
cdef int i
cdef int j
cdef int p
self.doAlignment()
j=self.xmax
i=self.vSeq.length
self.path=allocatePath(i,j+1,self.path)
if self.xmax<self.hSeq.length:
self.path.path[self.path.length]=self.vSeq.length-self.xmax
self.path.length+=1
while (i or j):
p=self.matrix.matrix[self.index(j,i)].path
self.path.path[self.path.length]=p
self.path.length+=1
#path.append(p)
if p==0:
i-=1
j-=1
elif p < 0:
i+=p
else:
j-=p
#path.reverse()
self.path.hStart=0
self.path.vStart=0
#reversePath(self.path)
#return 0,0,path
cdef class RightReverseAssemble(RightDirectAssemble):
property seqB:
def __get__(self):
return self.verticalSeq.wrapped
def __set__(self, seq):
self.sequenceChanged=True
self.verticalSeq=seq.complement()
self.vSeq=allocateSequence(self.verticalSeq,self.vSeq)

209
src/obitools/fastq/__init__.py Normal file
View File

@@ -0,0 +1,209 @@
'''
Created on 29 ao<61>t 2009
@author: coissac
'''
from obitools import BioSequence
from obitools.format.genericparser import genericEntryIteratorGenerator
from obitools import bioSeqGenerator,AASequence,NucSequence
from obitools.fasta import _parseFastaTag,parseFastaDescription
from _fastq import fastqQualitySangerDecoder,fastqQualitySolexaDecoder
from _fastq import qualityToSangerError,qualityToSolexaError
from _fastq import errorToSangerFastQStr
from obitools.utils import universalOpen
fastqEntryIterator=genericEntryIteratorGenerator(startEntry='^@',endEntry="^\+",strip=True,join=False)
def fastqParserGenetator(fastqvariant='sanger',bioseqfactory=NucSequence,tagparser=_parseFastaTag):
qualityDecoder,errorDecoder = {'sanger' : (fastqQualitySangerDecoder,qualityToSangerError),
'solexa' : (fastqQualitySolexaDecoder,qualityToSolexaError),
'illumina' : (fastqQualitySolexaDecoder,qualityToSangerError)}[fastqvariant]
def fastqParser(seq):
'''
Parse a fasta record.
@attention: internal purpose function
@param seq: a sequence object containing all lines corresponding
to one fasta sequence
@type seq: C{list} or C{tuple} of C{str}
@param bioseqfactory: a callable object return a BioSequence
instance.
@type bioseqfactory: a callable object
@param tagparser: a compiled regular expression usable
to identify key, value couples from
title line.
@type tagparser: regex instance
@return: a C{BioSequence} instance
'''
title = seq[0][1:].split(None,1)
id=title[0]
if len(title) == 2:
definition,info=parseFastaDescription(title[1], tagparser)
else:
info= {}
definition=None
quality=errorDecoder(qualityDecoder(seq[3]))
seq=seq[1]
seq = bioseqfactory(id, seq, definition,False,**info)
seq.quality = quality
return seq
return fastqParser
def fastqIterator(file,fastqvariant='sanger',bioseqfactory=NucSequence,tagparser=_parseFastaTag):
'''
iterate through a fasta file sequence by sequence.
Returned sequences by this iterator will be BioSequence
instances
@param file: a line iterator containing fasta data or a filename
@type file: an iterable object or str
@param bioseqfactory: a callable object return a BioSequence
instance.
@type bioseqfactory: a callable object
@param tagparser: a compiled regular expression usable
to identify key, value couples from
title line.
@type tagparser: regex instance
@return: an iterator on C{BioSequence} instance
@see: L{fastaNucIterator}
@see: L{fastaAAIterator}
'''
fastqParser=fastqParserGenetator(fastqvariant, bioseqfactory, tagparser)
file = universalOpen(file)
for entry in fastqEntryIterator(file):
title=entry[0]
seq="".join(entry[1:-1])
quality=''
while (len(quality) < len(seq)):
quality+=file.next().strip()
yield fastqParser([title,seq,'+',quality])
def fastqSangerIterator(file,tagparser=_parseFastaTag):
'''
iterate through a fastq file sequence by sequence.
Returned sequences by this iterator will be NucSequence
instances
@param file: a line iterator containint fasta data
@type file: an iterable object
@param tagparser: a compiled regular expression usable
to identify key, value couples from
title line.
@type tagparser: regex instance
@return: an iterator on C{NucBioSequence} instance
@see: L{fastqIterator}
@see: L{fastqAAIterator}
'''
return fastqIterator(file,'sanger',NucSequence,tagparser)
def fastqSolexaIterator(file,tagparser=_parseFastaTag):
'''
iterate through a fastq file sequence by sequence.
Returned sequences by this iterator will be NucSequence
instances
@param file: a line iterator containint fasta data
@type file: an iterable object
@param tagparser: a compiled regular expression usable
to identify key, value couples from
title line.
@type tagparser: regex instance
@return: an iterator on C{NucBioSequence} instance
@see: L{fastqIterator}
@see: L{fastqAAIterator}
'''
return fastqIterator(file,'solexa',NucSequence,tagparser)
def fastqIlluminaIterator(file,tagparser=_parseFastaTag):
'''
iterate through a fastq file sequence by sequence.
Returned sequences by this iterator will be NucSequence
instances
@param file: a line iterator containint fasta data
@type file: an iterable object
@param tagparser: a compiled regular expression usable
to identify key, value couples from
title line.
@type tagparser: regex instance
@return: an iterator on C{NucBioSequence} instance
@see: L{fastqIterator}
@see: L{fastqAAIterator}
'''
return fastqIterator(file,'illumina',NucSequence,tagparser)
def fastqAAIterator(file,tagparser=_parseFastaTag):
'''
iterate through a fastq file sequence by sequence.
Returned sequences by this iterator will be AASequence
instances
@param file: a line iterator containing fasta data
@type file: an iterable object
@param tagparser: a compiled regular expression usable
to identify key, value couples from
title line.
@type tagparser: regex instance
@return: an iterator on C{AABioSequence} instance
@see: L{fastqIterator}
@see: L{fastqNucIterator}
'''
return fastqIterator(file,'sanger',AASequence,tagparser)
def formatFastq(data,gbmode=False):
if isinstance(data, BioSequence):
data = [data]
rep = []
for sequence in data:
seq = str(sequence)
if sequence.definition is None:
definition=''
else:
definition=sequence.definition
info='; '.join(['%s=%s' % x for x in sequence.rawiteritems()])
if info:
info=info+';'
id = sequence.id
if gbmode:
if 'gi' in sequence:
id = "gi|%s|%s" % (sequence['gi'],id)
else:
id = "lcl|%s|" % (id)
if hasattr(sequence, "quality"):
quality=errorToSangerFastQStr(sequence.quality)
else:
quality="I"*len(sequence)
title='@%s %s %s' %(id,info,definition)
rep.append("%s\n%s\n+\n%s" % (title,seq,quality))
return '\n'.join(rep)

2915
src/obitools/fastq/_fastq.c Normal file
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File diff suppressed because it is too large Load Diff

156
src/obitools/fastq/_fastq.pyx Normal file
View File

@@ -0,0 +1,156 @@
'''
Created on 16 sept. 2009
@author: coissac
'''
from array import array
cdef import from "math.h" :
double log10(double x)
double rint(double x)
cdef import from "string.h":
int strlen(char* s)
cdef import from "stdlib.h":
void* malloc(int size) except NULL
void* realloc(void* chunk,int size) except NULL
void free(void* chunk)
cdef import from "string.h":
void bzero(void *s, size_t n)
cpdef object fastqQualityDecoder(char* qualstring, int base=0):
cdef int i=0
cdef int mq=255
cdef object quality
cdef object oaddresse,olength
cdef int length
cdef double* bdouble
quality = array('d',[0] * strlen(qualstring))
(oaddress,olength)=quality.buffer_info()
bdouble=<double*><unsigned long int>oaddress
if base==0:
mq = 255
while (qualstring[i]!=0):
if qualstring[i]<mq:
mq=qualstring[i]
i+=1
if mq < 59:
base=33
else:
base=64
i=0
while (qualstring[i]!=0):
bdouble[i]=qualstring[i]-base
i+=1
return quality
cpdef object fastqQualitySangerDecoder(char* qualstring):
return fastqQualityDecoder(qualstring,33)
cpdef object fastqQualitySolexaDecoder(char* qualstring):
return fastqQualityDecoder(qualstring,64)
cpdef object qualityToSolexaError(object quality):
cdef int i=0
cdef int lq
cdef double proba
cdef object oaddresse,olength
cdef int length
cdef double* bdouble
(oaddress,olength)=quality.buffer_info()
bdouble=<double*><unsigned long int>oaddress
lq=olength
for i in range(lq):
proba=1/(1+10.**(bdouble[i]/10.))
bdouble[i]=proba
return quality
cpdef object qualityToSangerError(object quality):
cdef int i=0
cdef int lq
cdef double proba
cdef object oaddresse,olength
cdef int length
cdef double* bdouble
(oaddress,olength)=quality.buffer_info()
bdouble=<double*><unsigned long int>oaddress
lq=olength
for i in range(lq):
proba=10.**(-bdouble[i]/10.)
bdouble[i]=proba
return quality
cpdef object errorToSangerQuality(object quality):
cdef int i=0
cdef int lq
cdef double proba
cdef object oaddresse,olength
cdef int length
cdef double* bdouble
(oaddress,olength)=quality.buffer_info()
bdouble=<double*><unsigned long int>oaddress
lq=olength
for i in range(lq):
proba=-rint(log10(bdouble[i])*10)
bdouble[i]=proba
return quality
cpdef object solexaToSangerQuality(object quality):
cdef int i=0
cdef int lq
cdef double proba
cdef object oaddresse,olength
cdef int length
cdef double* bdouble
(oaddress,olength)=quality.buffer_info()
bdouble=<double*><unsigned long int>oaddress
lq=olength
for i in range(lq):
proba=-rint(log10(1/(1+10.**(bdouble[i]/10.)))*10)
bdouble[i]=proba
return quality
cpdef object errorToSangerFastQStr(object quality):
cdef int i=0
cdef int lq
cdef double proba
cdef object oaddresse,olength
cdef int length
cdef double* bdouble
cdef char* result
cdef str code
(oaddress,olength)=quality.buffer_info()
bdouble=<double*><unsigned long int>oaddress
lq=olength
result=<char *>malloc(olength+1)
result[olength]=0
for i in range(lq):
proba=-rint(log10(bdouble[i])*10)
if proba > 93.:
proba=93.
result[i]=33 + <int>proba
code=result
free(<void *>result)
return code

14
src/obitools/format/genericparser/__init__.py
View File

@@ -5,7 +5,7 @@ import re
from obitools.utils import universalOpen
def genericEntryIteratorGenerator(startEntry=None,endEntry=None,head=False,tail=False,strip=False):
def genericEntryIteratorGenerator(startEntry=None,endEntry=None,head=False,tail=False,strip=False,join=True):
'''
Transfome a text line iterator to an entry oriented iterator.
@@ -62,10 +62,15 @@ def genericEntryIteratorGenerator(startEntry=None,endEntry=None,head=False,tail=
if end:
if endEntry is not None:
entry.append(line)
if join:
e = ''.join(entry)
entry=[]
if strip:
e=e.strip()
else:
e=entry
if strip:
e=[x.strip() for x in e]
entry=[]
yield e
started=False
if endEntry is not None:
@@ -78,9 +83,14 @@ def genericEntryIteratorGenerator(startEntry=None,endEntry=None,head=False,tail=
except StopIteration:
if entry and (endEntry is None or tail):
if join:
e = ''.join(entry)
if strip:
e=e.strip()
else:
e=entry
if strip:
e=[x.strip() for x in e]
yield e

22
src/obitools/location/__init__.py
View File

@@ -135,6 +135,8 @@ class SimpleLocation(Location):
self._begin = begin
self._end = end
self._before=False
self._after=False
def _extractSequence(self,sequence):
@@ -191,6 +193,26 @@ class SimpleLocation(Location):
begin = property(getBegin,None,None,"beginning position of the location")
end = property(getEnd,None,None,"ending position of the location")
def getBefore(self):
return self._before
def getAfter(self):
return self._after
def setBefore(self,value):
assert isinstance(value, bool)
self._before=value
def setAfter(self,value):
assert isinstance(value, bool)
self._after=value
before=property(getBefore,setBefore,None)
after=property(getAfter,setAfter,None)
class PointLocation(Location):
"""
A point location describes a location on a sequence

124
src/obitools/word/_binary.c
View File

@@ -1,4 +1,4 @@
/* Generated by Cython 0.11.3 on Fri Dec 18 14:54:07 2009 */
/* Generated by Cython 0.11.3 on Mon Jan 4 22:18:11 2010 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -427,10 +427,10 @@ static char __pyx_k_t[] = "t";
static PyObject *__pyx_kp_t;
static char __pyx_k_size[] = "size";
static PyObject *__pyx_kp_size;
static char __pyx_k_1[] = "w1";
static PyObject *__pyx_kp_1;
static char __pyx_k_2[] = "w2";
static PyObject *__pyx_kp_2;
static char __pyx_k_28[] = "w1";
static PyObject *__pyx_kp_28;
static char __pyx_k_29[] = "w2";
static PyObject *__pyx_kp_29;
static char __pyx_k_word[] = "word";
static PyObject *__pyx_kp_word;
static char __pyx_k_pattern[] = "pattern";
@@ -441,39 +441,39 @@ static char __pyx_k_xrange[] = "xrange";
static PyObject *__pyx_kp_xrange;
static char __pyx_k_join[] = "join";
static PyObject *__pyx_kp_join;
static char __pyx_k_5[] = "acgt";
static PyObject *__pyx_kp_5;
static char __pyx_k_32[] = "acgt";
static PyObject *__pyx_kp_32;
static char __pyx_k_lower[] = "lower";
static PyObject *__pyx_kp_lower;
static char __pyx_k_7[] = "c";
static PyObject *__pyx_kp_7;
static char __pyx_k_8[] = "g";
static PyObject *__pyx_kp_8;
static char __pyx_k_9[] = "t";
static PyObject *__pyx_kp_9;
static char __pyx_k_10[] = "a";
static PyObject *__pyx_kp_10;
static char __pyx_k_34[] = "c";
static PyObject *__pyx_kp_34;
static char __pyx_k_35[] = "g";
static PyObject *__pyx_kp_35;
static char __pyx_k_36[] = "t";
static PyObject *__pyx_kp_36;
static char __pyx_k_37[] = "a";
static PyObject *__pyx_kp_37;
static char __pyx_k_RuntimeError[] = "RuntimeError";
static PyObject *__pyx_kp_RuntimeError;
static char __pyx_k_12[] = "armwdhvn";
static PyObject *__pyx_kp_12;
static char __pyx_k_13[] = "cymsbhvn";
static PyObject *__pyx_kp_13;
static char __pyx_k_14[] = "grksbdvn";
static PyObject *__pyx_kp_14;
static char __pyx_k_15[] = "tykwbdhn";
static PyObject *__pyx_kp_15;
static char __pyx_k_39[] = "armwdhvn";
static PyObject *__pyx_kp_39;
static char __pyx_k_40[] = "cymsbhvn";
static PyObject *__pyx_kp_40;
static char __pyx_k_41[] = "grksbdvn";
static PyObject *__pyx_kp_41;
static char __pyx_k_42[] = "tykwbdhn";
static PyObject *__pyx_kp_42;
static PyObject *__pyx_builtin_bin;
static PyObject *__pyx_builtin_xrange;
static PyObject *__pyx_builtin_RuntimeError;
static PyObject *__pyx_kp_3;
static char __pyx_k_3[] = "(a:%s,c:%s,g:%s,t:%s)";
static PyObject *__pyx_kp_4;
static char __pyx_k_4[] = "";
static PyObject *__pyx_kp_6;
static PyObject *__pyx_kp_11;
static char __pyx_k_6[] = "Word length should be less or equal to 32";
static char __pyx_k_11[] = "word should only contain a, c, g or t (%s)";
static PyObject *__pyx_kp_30;
static char __pyx_k_30[] = "(a:%s,c:%s,g:%s,t:%s)";
static PyObject *__pyx_kp_31;
static char __pyx_k_31[] = "";
static PyObject *__pyx_kp_33;
static PyObject *__pyx_kp_38;
static char __pyx_k_33[] = "Word length should be less or equal to 32";
static char __pyx_k_38[] = "word should only contain a, c, g or t (%s)";
/* "/Users/coissac/encours/OBITools/src/obitools/word/_binary.pyx":15
*
@@ -695,7 +695,7 @@ static PyObject *__pyx_pf_8obitools_4word_7_binary_11WordPattern___str__(PyObjec
__pyx_t_2 = 0;
__pyx_t_3 = 0;
__pyx_t_4 = 0;
__pyx_t_4 = PyNumber_Remainder(__pyx_kp_3, ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = PyNumber_Remainder(__pyx_kp_30, ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
__pyx_r = __pyx_t_4;
@@ -926,7 +926,7 @@ static PyObject *__pyx_pf_8obitools_4word_7_binary_wordDist(PyObject *__pyx_self
unsigned PY_LONG_LONG __pyx_v_w2;
PyObject *__pyx_r = NULL;
PyObject *__pyx_t_1 = NULL;
static PyObject **__pyx_pyargnames[] = {&__pyx_kp_1,&__pyx_kp_2,0};
static PyObject **__pyx_pyargnames[] = {&__pyx_kp_28,&__pyx_kp_29,0};
__Pyx_SetupRefcountContext("wordDist");
__pyx_self = __pyx_self;
if (unlikely(__pyx_kwds)) {
@@ -940,11 +940,11 @@ static PyObject *__pyx_pf_8obitools_4word_7_binary_wordDist(PyObject *__pyx_self
}
switch (PyTuple_GET_SIZE(__pyx_args)) {
case 0:
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_kp_1);
values[0] = PyDict_GetItem(__pyx_kwds, __pyx_kp_28);
if (likely(values[0])) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
values[1] = PyDict_GetItem(__pyx_kwds, __pyx_kp_2);
values[1] = PyDict_GetItem(__pyx_kwds, __pyx_kp_29);
if (likely(values[1])) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("wordDist", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
@@ -2032,7 +2032,7 @@ static PyObject *__pyx_f_8obitools_4word_7_binary_decodeWord(unsigned PY_LONG_L
* cpdef int encodeWord(word) except -1:
*/
__Pyx_XDECREF(((PyObject *)__pyx_r));
__pyx_t_1 = PyObject_GetAttr(__pyx_kp_4, __pyx_kp_join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_1 = PyObject_GetAttr(__pyx_kp_31, __pyx_kp_join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
@@ -2085,7 +2085,7 @@ static PyObject *__pyx_f_8obitools_4word_7_binary_decodeWord(unsigned PY_LONG_L
__pyx_t_4 = PyNumber_And(__pyx_t_6, __pyx_int_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__pyx_1 = PyObject_GetItem(__pyx_kp_5, __pyx_t_4); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_1 = PyObject_GetItem(__pyx_kp_32, __pyx_t_4); if (!__pyx_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_7 = PyList_Append(__pyx_t_2, (PyObject*)__pyx_1); if (unlikely(__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -2234,7 +2234,7 @@ static int __pyx_f_8obitools_4word_7_binary_encodeWord(PyObject *__pyx_v_word,
#ifndef PYREX_WITHOUT_ASSERTIONS
__pyx_t_1 = PyObject_Length(__pyx_v_word); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (unlikely(!(__pyx_t_1 <= 32))) {
PyErr_SetObject(PyExc_AssertionError, __pyx_kp_6);
PyErr_SetObject(PyExc_AssertionError, __pyx_kp_33);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
@@ -2318,7 +2318,7 @@ static int __pyx_f_8obitools_4word_7_binary_encodeWord(PyObject *__pyx_v_word,
* w|=1
* elif l=='g':
*/
__pyx_t_2 = PyObject_RichCompare(__pyx_v_l, __pyx_kp_7, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = PyObject_RichCompare(__pyx_v_l, __pyx_kp_34, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -2346,7 +2346,7 @@ static int __pyx_f_8obitools_4word_7_binary_encodeWord(PyObject *__pyx_v_word,
* w|=2
* elif l=='t':
*/
__pyx_t_2 = PyObject_RichCompare(__pyx_v_l, __pyx_kp_8, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = PyObject_RichCompare(__pyx_v_l, __pyx_kp_35, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -2374,7 +2374,7 @@ static int __pyx_f_8obitools_4word_7_binary_encodeWord(PyObject *__pyx_v_word,
* w|=3
* elif l!='a':
*/
__pyx_t_2 = PyObject_RichCompare(__pyx_v_l, __pyx_kp_9, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = PyObject_RichCompare(__pyx_v_l, __pyx_kp_36, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -2402,7 +2402,7 @@ static int __pyx_f_8obitools_4word_7_binary_encodeWord(PyObject *__pyx_v_word,
* raise RuntimeError,"word should only contain a, c, g or t (%s)" % word
* return w
*/
__pyx_t_2 = PyObject_RichCompare(__pyx_v_l, __pyx_kp_10, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = PyObject_RichCompare(__pyx_v_l, __pyx_kp_37, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -2415,7 +2415,7 @@ static int __pyx_f_8obitools_4word_7_binary_encodeWord(PyObject *__pyx_v_word,
* return w
*
*/
__pyx_t_2 = PyNumber_Remainder(__pyx_kp_11, __pyx_v_word); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = PyNumber_Remainder(__pyx_kp_38, __pyx_v_word); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_builtin_RuntimeError, __pyx_t_2, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -2669,7 +2669,7 @@ static PyObject *__pyx_pf_8obitools_4word_7_binary_encodePattern(PyObject *__pyx
* a|=1
* if l in 'cymsbhvn':
*/
__pyx_t_4 = (PySequence_Contains(__pyx_kp_12, __pyx_v_l)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 176; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = (PySequence_Contains(__pyx_kp_39, __pyx_v_l)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 176; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_4) {
/* "/Users/coissac/encours/OBITools/src/obitools/word/_binary.pyx":177
@@ -2695,7 +2695,7 @@ static PyObject *__pyx_pf_8obitools_4word_7_binary_encodePattern(PyObject *__pyx
* c|=1
* if l in 'grksbdvn':
*/
__pyx_t_4 = (PySequence_Contains(__pyx_kp_13, __pyx_v_l)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = (PySequence_Contains(__pyx_kp_40, __pyx_v_l)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_4) {
/* "/Users/coissac/encours/OBITools/src/obitools/word/_binary.pyx":179
@@ -2721,7 +2721,7 @@ static PyObject *__pyx_pf_8obitools_4word_7_binary_encodePattern(PyObject *__pyx
* g|=1
* if l in 'tykwbdhn':
*/
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__pyx_t_4 = (PySequence_Contains(__pyx_kp_41, __pyx_v_l)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_4) {
/* "/Users/coissac/encours/OBITools/src/obitools/word/_binary.pyx":181
@@ -2747,7 +2747,7 @@ static PyObject *__pyx_pf_8obitools_4word_7_binary_encodePattern(PyObject *__pyx
* t|=1
*
*/
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{&__pyx_kp_t, __pyx_k_t, sizeof(__pyx_k_t), 1, 1, 1},
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{&__pyx_kp_word, __pyx_k_word, sizeof(__pyx_k_word), 1, 1, 1},
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static int __Pyx_InitCachedBuiltins(void) {

264
src/solexaPairEnd.py Normal file
View File

@@ -0,0 +1,264 @@
#!/usr/local/bin/python
'''
Created on 30 dec. 2009
@author: coissac
'''
from obitools.options import getOptionManager
from obitools.fastq import fastqSolexaIterator, formatFastq
from obitools.alignment import columnIterator
from obitools.align import QSolexaReverseAssemble
from obitools.align import QSolexaRightReverseAssemble
from array import array
from obitools import NucSequence
import sys
def addSolexaPairEndOptions(optionManager):
optionManager.add_option('-r','--reverse-reads',
action="store", dest="reverse",
metavar="<FILENAME>",
type="string",
default=None,
help="Filename containing reverse solexa reads "
)
def checkAlignOk(ali):
#print not (ali[0][0]=='-' or ali[1][len(ali[1])-1]=='-')
return not (ali[0][0]=='-' or ali[1][len(ali[1])-1]=='-')
def iterOnAligment(ali):
pos0=0
pos1=len(ali[1].wrapped)-1
begin0=False
end0=False
begin1=False
end1=False
for nuc0,nuc1 in columnIterator(ali):
if nuc0=='-':
if begin0:
if not end0:
score0 = ( ali[0].wrapped.quality[pos0-1]
+ali[0].wrapped.quality[pos0]
)/2
else:
score0 = 1.
else:
score0 = 0.
else:
begin0=True
score0 = ali[0].wrapped.quality[pos0]
pos0+=1
end0= pos0==len(ali[0].wrapped)
if nuc1=='-':
if begin1:
if not end1:
score1 = ( ali[1].wrapped.wrapped.quality[pos1]
+ali[1].wrapped.wrapped.quality[pos1+1]
)/2
else:
score1 = 0.
else:
score1 = 1.
else:
begin1=True
score1 = ali[1].wrapped.wrapped.quality[pos1]
pos1-=1
end1=pos1<0
result = (nuc0,score0,nuc1,score1)
yield result
class IterOnConsensus:
def __init__(self,ali):
self._ali=ali
self.__seqASingle=0
self.__seqBSingle=0
self.__seqABMatch=0
self.__seqAMismatch=0
self.__seqBMismatch=0
self.__seqAInsertion=0
self.__seqBInsertion=0
self.__seqADeletion=0
self.__seqBDeletion=0
def get_seqASingle(self):
return self.__seqASingle
def get_seqBSingle(self):
return self.__seqBSingle
def get_seqABMatch(self):
return self.__seqABMatch
def get_seqAMismatch(self):
return self.__seqAMismatch
def get_seqBMismatch(self):
return self.__seqBMismatch
def get_seqAInsertion(self):
return self.__seqAInsertion
def get_seqBInsertion(self):
return self.__seqBInsertion
def get_seqADeletion(self):
return self.__seqADeletion
def get_seqBDeletion(self):
return self.__seqBDeletion
def __iter__(self):
firstSeqB=False
for nuc0,score0,nuc1,score1 in iterOnAligment(ali):
if nuc0==nuc1:
if nuc1!='-':
firstSeqB=True
self.__seqABMatch+=1
self.__seqBSingle=0
yield (nuc0,score0*score1)
else:
h0 = score0 * (1-score1/3)
h1 = score1 * (1-score0/3)
if h0 < h1:
if nuc0!='-':
self.__seqBSingle=0
if nuc1=='-':
if firstSeqB:
self.__seqAInsertion+=1
else:
self.__seqASingle+=1
else:
firstSeqB=True
self.__seqAMismatch+=1
yield (nuc0,h0)
else:
self.__seqADeletion+=1
else:
if nuc1!='-':
firstSeqB=True
if nuc0=='-':
self.__seqBInsertion+=1
self.__seqBSingle+=1
else:
self.__seqBMismatch+=1
self.__seqBSingle=0
yield (nuc1,h1)
else:
self.__seqBSingle=0
self.__seqBDeletion+=1
seqASingle = property(get_seqASingle, None, None, "direct's docstring")
seqBSingle = property(get_seqBSingle, None, None, "reverse's docstring")
seqABMatch = property(get_seqABMatch, None, None, "idem's docstring")
seqAMismatch = property(get_seqAMismatch, None, None, "mismatchdirect's docstring")
seqBMismatch = property(get_seqBMismatch, None, None, "mismatchreverse's docstring")
seqAInsertion = property(get_seqAInsertion, None, None, "insertdirect's docstring")
seqBInsertion = property(get_seqBInsertion, None, None, "insertreverse's docstring")
seqADeletion = property(get_seqADeletion, None, None, "deletedirect's docstring")
seqBDeletion = property(get_seqBDeletion, None, None, "deletereverse's docstring")
def iterOnConsensus(ali):
for nuc0,score0,nuc1,score1 in iterOnAligment(ali):
if nuc0==nuc1:
if nuc1!='-':
op='m'
yield (nuc0,score0*score1)
else:
h0 = score0 * (1-score1/3)
h1 = score1 * (1-score0/3)
if h0 < h1:
if nuc0!='-':
if nuc1=='-':
op="d"
else:
op='s'
yield (nuc0,h0)
else:
if nuc1!='-':
if nuc0=='-':
op="i"
else:
op='s'
yield (nuc1,h1)
def buildConsensus(ali):
seq=[]
quality=array('d')
ic=IterOnConsensus(ali)
for nuc,score in ic:
seq.append(nuc)
quality.append(score)
seq=''.join(seq)
seq=NucSequence(ali[0].wrapped.id+'_CONS',seq,**ali[0].wrapped.getTags())
seq.quality=quality
if hasattr(ali, "direction"):
seq['alignment']=ali.direction
seq['seqASingle']=ic.seqASingle
seq['seqBSingle']=ic.seqBSingle
seq['seqABMatch']=ic.seqABMatch
seq['seqAMismatch']=ic.seqAMismatch
seq['seqBMismatch']=ic.seqBMismatch
seq['seqAInsertion']=ic.seqAInsertion
seq['seqBInsertion']=ic.seqBInsertion-ic.seqBSingle
seq['seqADeletion']=ic.seqADeletion
seq['seqBDeletion']=ic.seqBDeletion
return seq
def buildAlignment(direct,reverse):
la = QSolexaReverseAssemble()
ra = QSolexaRightReverseAssemble()
for d in direct:
r = reverse.next()
la.seqA=d
la.seqB=r
ali=la()
ali.direction='left'
if not checkAlignOk(ali):
# print >>sys.stderr,"-> bad : -------------------------"
# print >>sys.stderr,ali
# print >>sys.stderr,"----------------------------------"
ra.seqA=d
ra.seqB=r
ali=ra()
ali.direction='right'
# print >>sys.stderr,ali
# print >>sys.stderr,"----------------------------------"
yield ali
if __name__ == '__main__':
optionParser = getOptionManager([addSolexaPairEndOptions],
entryIterator=fastqSolexaIterator
)
(options, direct) = optionParser()
reverse = fastqSolexaIterator(options.reverse)
for ali in buildAlignment(direct, reverse):
consensus = buildConsensus(ali)
print formatFastq(consensus)